Single-cell genomics (SCG) appeared as a powerful technique to get genomic information from uncultured organisms. However, SCG techniques suffer from biases at the whole genome amplification step that can lead to extremely variable numbers of genome recovery (5-100%). Thus, it is unclear how useful can SCG be to address evolutionary questions on uncultured microbial eukaryotes. To provide some insights into this, we here analysed 3 single-cell amplified genomes (SAGs) of the choanoflagellate Monosiga brevicollis, whose genome is known. Our results show that each SAG has a different, independent bias, yielding different levels of genome recovery for each cell (6-36%). Genes often appear fragmented and are split into more genes during annotation. Thus, analyses of gene gain and losses, gene architectures, synteny and other genomic features can not be addressed with a single SAG. However, the recovery of phylogenetically-informative protein domains can be up to 55%. This means SAG data can be used to perform accurate phylogenomic analyses. Finally, we also confirm that the co-assembly of several SAGs improves the general genomic recovery. Overall, our data show that, besides important current limitations, SAGs can still provide interesting and novel insights from poorly-known, uncultured organisms.

We acknowledge support by ICREA, a European Research Council Consolidator (ERC-2012-Co-616960) grant, and grant (BFU2014-57779-P) from Ministerio de Economía y Competitividad (MINECO) with FEDER funds. We also acknowledge financial support from Secretaria d'Universitats i Recerca del Departament d'Economia i Coneixement de la Generalitat de Catalunya (Project 2014 SGR 619). The authors want to acknowledge Jean-Francois Mangot for the support on the tetranucleotide frequency calculations and Ramon Massana for helpful discussions on the manuscript. We also thank Javier del Campo for some initial ideas, further discussions, and help in the experimental design. Any opinion, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. We also thank the commitment of the following people and sponsors: CNRS (in particular Groupement de Recherche GDR3280), European Molecular Biology Laboratory (EMBL), Genoscope/CEAthe French Government 'Investissements d'Avenir' programmes OCEANOMICS (ANR-11-BTBR-0008) and FRANCE GENOMIQUE (ANR-10-INBS-09-08), Agence Nationale de la Recherche, and European Union FP7 (MicroB3/No.287589), We also thank the support and commitment of Agnès B. and Etienne Bourgois, the Veolia Environment Foundation, Region Bretagne, Lorient Agglomeration, World Courier, Illumina, the Eléctricité de France (EDF) Foundation, Fondation pour la recherche sur la biodiversité (FRB), the Foundation Prince Albert II de Monaco, the Tara Foundation, its schooner and teams. We thank MERCATOR-CORIOLIS and ACRI-ST for providing daily satellite data during the expedition. We are also grateful to the French Ministry of Foreign Affairs for supporting the expedition and to the countries who graciously granted sampling permissions. Tara Oceans would not exist without continuous support from 23 institutes (http://oceans.taraexpeditions.org/en/m/science/labs-involved/).